breseq  version 0.29.0  revision 8f9c342918e4
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsqtrim-IND_KHP_HOT_A9_F124_I0_R1_S40_L004_R2_0013,857,891384,481,808100.0%99.7 bases100 bases93.1%
errorsqtrim-IND_KHP_HOT_A9_F124_I0_R1_S40_L004_R1_0013,857,917385,652,153100.0%100.0 bases100 bases94.7%
total7,715,808770,133,961100.0%99.8 bases100 bases93.9%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652155.32.898.1%Escherichia coli str. K-12 substr. MG1655, complete genome.
total4,641,652100.0%

fit dispersion is the ratio of the variance to the mean for the negative binomial fit. It is =1 for Poisson and >1 for over-dispersed data.

New Junction Evidence

Junction Candidates Tested

optionlimitactual
Number of alignment pairs examined for constructing junction candidates≤ 100000100045
Coverage evenness (position-hash) score of junction candidates≥ 2≥ 4
Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold100 ≤ n ≤ 5000685
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.031

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.52593

pr(no read start) is the probability that there will not be an aligned read whose first base matches a given position on a given strand.

Final Junction Predictions

optionvalue
Coverage evenness (position-hash) score of predicted junctions must be≥ 3
Skew score of predicted junction (−log10 probability of unusual coverage evenness) must be≤ 0
Number of bases that at least one read must overlap each uniquely aligned side of a predicted junction≥ 6

Read Alignment Evidence

optionvalue
ModeFull Polymorphism
Ploidy1 (haploid)
Consensus mutation E-value cutoff10
Consensus frequency cutoffOFF
Consensus minimum coverage each strandOFF
Polymorphism E-value cutoff2
Polymorphism frequency cutoff0.15
Polymorphism minimum coverage each strand2
Polymorphism bias cutoffOFF
Predict indel polymorphismsYES
Skip indel polymorphisms in homopolymers runs of ≥3 bases
Skip base substitutions when they create a homopolymer flanked on each side by ≥2 bases

Execution Times

stepstartendelapsed
Read and reference sequence file input06:08:34 14 Jan 201706:10:00 14 Jan 20171 minute 26 seconds
Read alignment to reference genome06:10:01 14 Jan 201706:13:43 14 Jan 20173 minutes 42 seconds
Preprocessing alignments for candidate junction identification06:13:43 14 Jan 201706:16:27 14 Jan 20172 minutes 44 seconds
Preliminary analysis of coverage distribution06:16:27 14 Jan 201706:19:28 14 Jan 20173 minutes 1 second
Identifying junction candidates06:19:28 14 Jan 201706:21:10 14 Jan 20171 minute 42 seconds
Re-alignment to junction candidates06:21:10 14 Jan 201706:21:56 14 Jan 201746 seconds
Resolving alignments with junction candidates06:21:56 14 Jan 201706:26:31 14 Jan 20174 minutes 35 seconds
Creating BAM files06:26:31 14 Jan 201706:28:18 14 Jan 20171 minute 47 seconds
Tabulating error counts06:28:18 14 Jan 201706:31:34 14 Jan 20173 minutes 16 seconds
Re-calibrating base error rates06:31:34 14 Jan 201706:31:34 14 Jan 20170 seconds
Examining read alignment evidence06:31:34 14 Jan 201708:15:13 14 Jan 20171 hour 43 minutes 39 seconds
Polymorphism statistics08:15:13 14 Jan 201708:15:18 14 Jan 20175 seconds
Output08:15:18 14 Jan 201708:16:20 14 Jan 20171 minute 2 seconds
Total 2 hours 7 minutes 45 seconds